I don't have a save unfortunately. I was just relying on my auto-saves as back-ups and didn't think to take one.
In one of the cases (the germans) they had adopted buddism as well, and trying to get her to do anything to them was a "we couldn't betray out closest friends". I understand that. Same goes for civilizations that were on the other continents, I got a "We would have nothing to gain" message which I understand.
But the other 2 civ's on our continent (the greeks and the indians) were both running hindisum so they weren't pals with Isabella, but I still got the "We just don't like you enough" message from Isabella when trying to make her attack them. When defensive pacts became an option she wouldn't sign one with me for the same reason.
However, playing the game through, I was playing with PA enabled (was actually hoping to get Isabella into one since I had so many positives with her and I've never actually been diplomatic enough to have an AI PA with me) she formed a PA with Bismarck shortly after they became an option. She was pretty friendly with Bismarck (+11 or so on the quick glance sheet) but still far behind me in total positives. But I'm guessing regardless of that she just liked Bismarck better.
Oh well. Once that happened I was pretty pissed, rushed to tanks and wiped out Bismarck and put the hurt into Isabella before winning a diplo victory.
Edit:
Might be worth mentioning, I had it set to aggressive AI's (had never tried it before, wanted to see what it was like) and on noble difficulty level. Dunno if that makes a difference.